On Thu, Sep 17, 2009 at 4:43 PM, Michael Lawrence <[email protected]>wrote:
> On Thu, Sep 17, 2009 at 8:14 AM, Ivan Gregoretti <[email protected]> > wrote: > > > Hello everybody > > > > How do you convert BED formatted files to WIG files? > > > > > > I tried to do that with rtracklayer but it didn't quite succeed. > > > > This is the session's transcript: > > > > First, you can download > > http://dl.getdropbox.com/u/2051155/myRegions.bed, which looks like > > this > > > > chr1 3002444 3002479 + > > chr1 3002989 3003024 - > > chr1 3017603 3017638 + > > chr1 3017879 3017914 - > > chr1 3018173 3018208 + > > chr1 3018183 3018218 - > > chr1 3018183 3018218 - > > chr1 3019065 3019100 + > > chr1 3019761 3019796 - > > chr1 3020044 3020079 - > > ... > > > > Now to R > > > > suppressMessages(library(rtracklayer)) > > myRegions <- import('myRegions.bed') > > > > So far so good. Now I try: > > export(myRegions, 'myRegions.wig', format = 'wig') > > > > but I get: > > Error in export.ucsc(object, con, subformat, ...) : > > Track not compatible with WIG format: Overlapping features must be > > on separate strands and every feature width must be positive > > > > I seems that the error message is a feature rather than a bug. My > > interpretation is that export() does not like records like lines 6 and > > 7: > > chr1 3018183 3018218 - > > chr1 3018183 3018218 - > > > > So, how do you convert BED to WIG in your everyday work? > > > > > Well, as rtracklayer said, this track is not representable by WIG, which is > meant to communicate a single data value for a given genomic region (to > generate the bar plots in the UCSC browser, for instance). There aren't any > scores in your file, so why do you want to use WIG? > > Just guessing, here, but you may want to calculate coverage() first, Ivan? Sean > > Thank you, > > > > Ivan > > > > > sessionInfo() > > R version 2.9.2 (2009-08-24) > > x86_64-redhat-linux-gnu > > > > locale: > > > > > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C > > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > > > other attached packages: > > [1] rtracklayer_1.4.0 RCurl_0.94-1 > > > > loaded via a namespace (and not attached): > > [1] Biobase_2.4.0 Biostrings_2.12.0 BSgenome_1.12.0 IRanges_1.2.0 > > [5] tools_2.9.2 XML_2.3-0 > > > > Ivan Gregoretti, PhD > > National Institute of Diabetes and Digestive and Kidney Diseases > > National Institutes of Health > > 5 Memorial Dr, Building 5, Room 205. > > Bethesda, MD 20892. USA. > > Phone: 1-301-496-1592 > > Fax: 1-301-496-9878 > > > > _______________________________________________ > > Bioc-sig-sequencing mailing list > > [email protected] > > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
